Climate change is intensifying drought events, putting global food production under pressure. Within the EU-funded TOLERATE project, Work Package 3 (WP3), led by Bioclear earth, and in collaboration with Heriot-Watt University (HWU) we explore a promising and innovative solution: bioaugmentation—the addition of beneficial microorganisms to soil to improve plant health and stress tolerance.
What sets WP3 apart is the introduction of engineered bacteria carrying ancient genetic traits—DNA segments from microbes that evolved in extreme, hot environments long ago. These traits are believed to support survival under drought and heat stress. By combining synthetic biology with ecological understanding, WP3 aims to test whether these engineered microbes can help crops perform better under real agricultural conditions without disrupting the native microbial communities already present in soil.
This article highlights our strategy in WP3, focusing on controlled environment chamber experiments that assess how natural and engineered bacteria can support crop performance under drought—one of the most pressing concerns in European agriculture today.
The evolution of bioaugmentation: From pollution cleanup to crop boosters
Bioaugmentation, the strategic introduction of beneficial microbes—has traditionally been used to clean up contaminated environments by breaking down harmful pollutants. However, its potential extends well beyond clean-up. In agriculture, specific microorganisms can:
- Enhance nutrient availability
- Promote plant growth and higher yields
- Improve stress tolerance, during extreme weather leading to drought and salinity
In WP3, we take this concept a step further by introducing engineered bacterial strains – carrying ancient genetic traits that helped organisms survive extreme environmental stress-in real-world farming conditions. Our goal is to evaluate whether these novel inoculants can boost crop yields during drought while maintaining harmony with native soil microbial ecosystems.
The Role of WP3 in the TOLERATE Project
Bioclear earth (BCE), based in the Netherlands, leads WP3 and focuses on evaluating the ecological impact of introducing novel microbes into soil. Using molecular biology tools, BCE assesses how added bacteria interact with the existing microbial community, ensuring that beneficial functions are preserved or even enhanced.
They are joined by Heriot-Watt University (HWU) in the UK, which conducts controlled chamber experiments to test different microbial inoculants under drought stress.
Together, we aim to identify microbial strains that:
- Persist in the soil
- Promote plant growth
- Coexist with, or support, native beneficial microbes
Natural strains first: Pseudomonas as a bioaugmentation model
Before testing engineered bacteria, the team began with naturally occurring Pseudomonas strains, already known for their plant growth-promoting effects. HWU tested several species to evaluate their ability to enhance seed germination and early growth under salt and osmotic stress.
Key results:
- All strains improved plant performance compared to uninoculated controls
- Two strains stood out and were selected for drought-focused experiments
In a controlled drought stress experiment, barley plants were grown in soil with or without Pseudomonas inoculation. After an initial 5-day watering phase, drought stress was simulated by withholding watering for 14 days.
Outcomes:
- Inoculated barley plants showed 67% more shoot growth than droughted controls
- Chlorophyll, proline, and soluble sugar levels were higher—markers of improved drought resilience
- Even natural strains demonstrated a protective effect under water stress
Tracking microbial impact in soil
To monitor how these added microbes affect the natural microbial community, Bioclear earth analysed soil and rhizosphere samples from HWU’s experiments using Next-Generation Sequencing (NGS).
Preliminary insights:
- Bioaugmented soils had higher levels of the introduced Pseudomonas strain during drought
- These levels declined after re-watering, indicating temporary colonization
- Remarkably, the introduced strain appeared to support other beneficial microbes under stress
These findings suggest a synergistic effect between the added and native microbes, though repeated inoculation may be needed to sustain long-term benefits.
What comes next: engineered strains in more realistic conditions
The ultimate aim of WP3 is to test and evaluate engineered bacterial strains carrying ancient DNA from microbes that survived intense heat and drought conditions millions of years ago.
We are now transitioning to test these advanced inoculants first in the lab and then in chamber experiments to better reflect agricultural conditions. The focus will be on barley and other model crops.
Key questions we’re addressing:
- Will engineered microbes outperform natural strains in boosting plant resilience?
- Can they establish and persist in soil ecosystems?
- Will they cooperate with or disturb existing microbial communities?
These answers are essential before scaling bioaugmentation strategies to field-level agriculture.
Why bioaugmentation research Matters
WP3 supports EU goals for climate-resilient agriculture and sustainable food systems. By bridging natural and synthetic biology, this research aims to develop scalable, science-based solutions that:
- Reduce crop losses caused by drought, especially in vulnerable farming areas
- Minimize reliance on chemical fertilizers and pesticides
- Preserve or enhance microbial biodiversity in soils
Conclusion
Bioaugmentation represents a nature-based, forward-thinking solution to support optimal crops yields in an era of climate uncertainty. WP3 is testing both natural and engineered microbial inoculants to ensure they enhance drought resilience without harming soil ecosystems. This work is not just about microbes—it’s about creating a more sustainable, resilient future for European agriculture.
Follow our groundbreaking EU TOLERATE research, unlocking millions of years of microbial evolution to protect crops from climate change impacts.”
By Afnan Suleiman